Christian Vernière

Cirad - La recherche agronomique pour le développement | CIRAD · Unité Mixte de Recherche Biologie et Génétique des Interactions Plantes-Parasites (BGPI)

Cassava (Manihot esculenta Crantz) is a primary crop for food security of millions of people worldwide. In Colombia, the Caribbean region contributes about half of the national cassava production, despite major socioeconomic constraints such as unequal land property, omnipresence of middlemen, low and unstable prices, armed conflict, climate change...

Biomonitoring ecosystems is necessary in order to evaluate risks and to efficiently manage ecosystems and their associated services. Agrosystems are the target of multiple stressors that can affect many species through effects cascading along food webs. However, classic biomonitoring, focused on species diversity or indicator species, might be a po...

A thorough knowledge of genotypic and phenotypic variations (e.g., virulence, resistance to antimicrobial compounds) in bacteria causing plant disease outbreaks is key for optimizing disease surveillance and management. Using a comprehensive strain collection, tandem repeat-based genotyping techniques and pathogenicity assays, we characterized the...

The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infect...

Bacterial spot of pepper and tomato is caused by at least three species of Xanthomonas, among them two pathovars of Xanthomonas euvesicatoria, which are responsible for significant yield losses on all continents. In order to trace back the spread of bacterial spot pathogens within and among countries, we developed the first multilocus variable numb...

The Honghe Hani rice terraces system (HHRTS) is a traditional rice cultivation system where Hani people cultivate remarkably diverse rice varieties. Recent introductions of modern rice varieties to the HHRTS have significantly increased the severity of rice diseases within the terraces. Here we determine the impacts of these recent introductions on...

Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensive...

Background: Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen’s diversity and population structure are prerequisite for epidemiological surveillance and efficient disease management. Rapidly evolving genetic loci, such as Clustered...

Southern rice black-streaked dwarf virus (SRBSDV), which causes severe disease symptoms in rice (Oriza sativa L.) has been emerging in the last decade throughout northern Vietnam, southern Japan and southern, central and eastern China. Here we attempt to quantify the prevalence of SRBSDV in the Honghe Hani rice terraces system (HHRTS)—a Chinese 130...

Although some plant pathogenic bacteria represent a significant threat to agriculture, the determinants of their ecological success and evolutionary potential are still poorly understood. Refining our understanding of bacterial strain circulation at small spatial scales and the biological significance and evolutionary consequences of co-infections...

Diverse molecular markers have been used to analyze the genetic diversity of plant pathogens. Compared with traditional fingerprinting methods, multiple loci variable number of tandem repeat analyses (MLVAs) have gained importance recently due to their reproducibility, high discriminatory power, ease of performance, low cost, and throughput potenti...

Xanthomonas vasicola pv. musacearum (Xvm) which causes Xanthomonas wilt (XW) on banana (Musa accuminata x balbisiana) and enset (Ensete ventricosum), is closely related to the species Xanthomonas vasicola that contains the pathovars vasculorum (Xvv) and holcicola (Xvh), respectively pathogenic to sugarcane and sorghum. Xvm is considered a monomorph...

MLVA-19 alleles in X.vasicola pv. musacearum: Summary of allele sizes and correspondence with raw number of repeats and rounded number of repeats. The alleles shared with other pathovars of X.vasicola are indicated in the column “shared with”. Xvv: X.vasicola pv. vasculorum; Xvh: X.vasicola pv. holcicola. a Raw repeat numbers were rounded to the ne...

Relationship between VNTR loci repeat sizes and locus polymorphism, as assessed by Nei’s gene diversity (A) and number of alleles (B). (EPS)

Relative contributions (A) and correlations (B) of each variable (locus) to each of the first 5 dimensions of the PCA (R::FactoMineR::PCA). (XLSX)

Composition of clonal complexes obtained from a collection of Xanthomonas vasicola pv. musacearum (n = 335) with their number of haplotypes and countries of origin. (XLSX)

TR Loci characteristics: Motif sequence, array homogeneity and completeness. aThe nucleotides differing from the reference TR sequence are written in bold. b Occurrence frequency of the alternative TR sequence. (XLSX)

Comparison of the haplotypes obtained from a core-collection of 36 Xvm strains using the MLVA-19 scheme and the two sets of SNP-derived RFLP markers and their discriminative Hunter-Gaston index. (XLSX)

Physical positions of the MLVA-19 loci on the chromosome of the Xvm complete genome NCPPB 4379. Loci are designated by their name, and their coordinates on the chromosome. The intragenic loci are framed. (EPS)

Principal Component Analysis (PCA) showing the correlation circle of each variable to the MLVA-19 scheme on the most informative axes 1 and 2. (EPS)

Principal Component Analysis (PCA) showing the correlation circle of each variable to the MLVA-19 scheme on the most informative axes 1 and 3. (EPS)

Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk...

We describe the development of a new genotyping method on Xanthomonas vasicola pv musacearum (Xvm), the causing agent of Ensete/banana Xanthomonas Wilt, based on Multi Locus variable number of tandem repeats Analysis (MLVA), to understand its population structure and diversity at different time and spatial scales. Mining nine publicly available Xvm...

The Ralstonia solanacearum species complex (RSSC) is a highly diverse cluster of bacterial strains found worldwide, many of which are destructive and cause bacterial wilt (BW) in a wide range of host plants. In 2009, potato production in Madagascar was dramatically affected by several BW epidemics. Controlling this disease is critical for Malagasy...

The gammaproteobacterium Xanthomonas citri pv . citri causes Asiatic citrus canker. Pathotype A strains have a broad host range, which includes most commercial citrus species, and they cause important economic losses worldwide. Control often relies on frequent copper sprays. We present here the complete genomes of six X. citri pv . citri copper-res...

Copper-based antimicrobial compounds are widely used to control plant bacterial pathogens. Pathogens have adapted in response to this selective pressure. Xanthomonas citri pv. citri, a major citrus pathogen causing Asiatic citrus canker, was first reported to carry plasmid-encoded copper resistance in Argentina. This phenotype was conferred by the...

Multiple-Locus Variable Number Tandem Repeat Analysis (MLVA) is being used to analyze genetic diversity in phytopathogenic microorganisms. One of the most important pathogens affecting Cassava crops is Xanthomonas axonopodis pv. manihotis (Xam) as its infection relates to high loses in crop productivity. Several studies have reported that Xam popul...

Xanthomonas citri pv. citri causes Asiatic citrus canker (ACC), which induces erumpent, callus-like lesions on all aerial organs, and consequently defoliation, premature fruit drop, and twig dieback under high inoculum pressure. Present in most tropical and subtropical citrus producing regions, the disease can lead to important decreases in yield a...

Xanthomonas citri pv. mangiferaeindicae, causal agent of bacterial canker (or bacterial black spot), is a major pathogen of mango. The bacterium infects leaves, twigs, and fruit on a wide range of mango cultivars with severe defoliation and up to 80% in fruit losses (Gagnevin and Pruvost 2001). Bacterial canker has recently emerged in western Afric...

X. arboricola pv. pruni strains from international collections. (PDF)

Nucleotide sequence in Xanthomonas arboricola pv. pruni strain CFBP 3894 of TR loci that were excluded from the analysis or for which new primer combinations were designed. (PDF)

Xanthomonas arboricola pv. pruni strains isolated from 11 provinces in Spain. (PDF)

Xanthomonas arboricola pv. pruni is the causal agent of the bacterial spot disease of stone fruits, almond and some ornamental Prunus species. In Spain it was first detected in 2002 and since then, several outbreaks have occurred in different regions affecting mainly Japanese plum, peach and almond, both in commercial orchards and nurseries. As the...

How pathogens coevolve with and adapt to their hosts are critical to understanding how host jumps and/or acquisition of novel traits can lead to new disease emergences. The Xanthomonas genus includes Gram-negative plant-pathogenic bacteria that collectively infect a broad range of crops and wild plant species. However, individual Xanthomonas strain...

Asiatic canker, caused by Xanthomonas citri pv. citri, is a major threat to worldwide citriculture. Three pathotypes differing in host range and hypersensitive reactions toward citrus species have been defined. Whereas pathotypes Aw and A* have a restricted host range, X. citri pv. citri pathotype A infects a broader range including most commercial...

Xanthomonas citri pv. mangiferaeindicae is the causal agent of bacterial canker of mango (Mangifera indica, Anacardiaceae), a disease of international importance. Since the original description of the bacterium in the 1940s, the status of cashew (Anacardium occidentale, Anacardiaceae) as a host species has been unclear. Here, we report the first ou...

Bacterial canker (or bacterial black spot) caused by Xanthomonas citri pv. mangiferaeindicae is a disease threat for mango in tropical and subtropical countries (Gagnevin and Pruvost 2001). X. citri pv. mangiferaeindicae causes severe infection in a wide range of mango cultivars and induces slightly raised, angular, black leaf lesions, sometimes wi...

Molecular epidemiology studies further our understanding of migrations of phytopathogenic bacteria, the major determining factor in their emergence. Asiatic citrus canker, caused by Xanthomonas citri pv. citri, was recently reported in Mali and Burkina Faso, a region remote from other contaminated areas. To identify the origin and pathways of these...

Multilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars of Xanthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused by X. oryzae pv. oryz...

Xanthomonas oryzae : MLVA-16 repeat translation.

Table S1: Xanthomonas oryzae strains used in this study. Table S2: Characteristics of 33 sequenced VNTR loci. Table S3: Allelic richness and private allelic richness per locus and per lineage. Table S4: DAPC groups per lineage and number of strains originating from the different countries. Figure S1: Physical positions of 16 VNTR loci on the chrom...

Xanthomonas citri pv. mangiferaeindicae causing bacterial canker (or black spot) is a major mango (Mangifera indica L.) pathogen in tropical and subtropical areas (3). The bacterium infects a wide range of mango cultivars, and induces raised, angular, black leaf lesions, sometimes with a yellow chlorotic halo. Fruit symptoms first appear as small w...

The causal agent of Asiatic citrus canker, Xanthomonas citri pv. citri, is a bacterium of major economic importance in tropical and subtropical citrus-producing areas. X. citri pv. citri pathotype A can cause severe infection in a wide range of citrus species and induces erumpent, callus-like lesions with water-soaked margins evolving to corky cank...

West Asia has been recognized as a major centre for the diversification of Xanthomonas citri pv. citri, a citrus quarantine pathogen of considerable economic importance. However, little genotyping data is available mainly due to the paucity of microbial resources in this region. Using a comprehensive strain collection, several genotyping techniques...

We report here the draft genome sequence of Xanthomonas axonopodis pv. allii strain CFBP 6369, the causal agent of bacterial blight of onion. The draft genome has a size of 5,425,942 bp and a G+C content of 64.4%.

MultiLocus Variable number of tandem repeat Analysis (MLVA) has been extensively used to examine epidemiological and evolutionary issues on monomorphic human pathogenic bacteria, but not on bacterial plant pathogens of agricultural importance albeit such tools would improve our understanding of their epidemiology, as well as of the history of epide...

Worldwide Xanthomonas citri pv. citri strain collection used in this study.

Strains of Xanthomonas citri pv. citri originating from the New World used as supplementary individuals in the Discriminant Analysis of Principal Components (see Materials & Methods for details).

Categorical minimum spanning tree from MLVA-12 data (129 strains – 64 haplotypes) representing the genetic diversity within a worldwide strain collection of Xanthomonas citri pv. citri in relation with its pathological diversity.

Investigating the population biology of plant pathogens in their native areas is essential to understand the factors that shape their population structure and favour their spread. Monomorphic pathogens dispatch extremely low genetic diversity in invaded areas, and native areas constitute a major reservoir for future emerging strains. One of these,...

Asiatic citrus canker, caused by Xanthomonas citri pv. citri, is a bacterial disease of major economic importance in tropical and subtropical citrus-producing areas. X. citri pv. citri pathotype A can cause severe infection in a wide range of citrus species and induces erumpent, callus-like lesions with water-soaked margins evolving to corky canker...

Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus sug...

Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences. Comparative...

Asiatic citrus canker, caused by Xanthomonas citri pv. citri, is a bacterial disease of major economic importance in tropical and subtropical citrus-producing areas. X. citri pv. citri pathotype A can cause severe infection in a wide range of citrus species and induces erumpent, callus-like lesions with water-soaked margins evolving to corky canker...